This realease is the one used to build ATHEM resource https://lipm-browsers.toulouse.inra.fr/pub/ATHEM/ (2023, to be published) with the following parameters:
```params {
wt_genotype = 'WT'
trimmo_params = ' -validatePairs -phred33 '
trimmo_leading_qual_min = 20
trimmo_trailing_qual_min = 20
trimmo_sliding_window_size = 4
trimmo_sliding_window_qual = 20
trimmo_min_length = 50
aln_filter_mode = 'paired_rmdup'
samtools_max_memory = '8G'
mpileup_parameters = ' -B --max-depth 100 '
mpileuprecall_parameters = '-B'
varscan_mutant_min_coverage = 3
varscan_mutant_min_reads2 = 3
varscan_mutant_avg_qual = 30
varscan_mutant_var_freq = 0.01
varscan_mutant_var_freq_for_hom = 0.8
varscan_mutant_pvalue = 0.01
varscan_wt_min_coverage = 5
varscan_wt_min_reads2 = 4
varscan_wt_avg_qual = 30
varscan_wt_var_freq = 0.01
varscan_wt_var_freq_for_hom = 0.8
varscan_wt_pvalue = 0.01
min_line_wt_position = 3
min_line_mutant_position = 1
snpeff_up_downstream_len = 1000
//ANN[*] !~ "${snpeff_exclude_ann}"
snpeff_exclude_ann = 'LOW\\|intergenic_variant\\|upstream_gene_variant\\|intergenic_region'
}
```
and the following tools:
```
#software version
bcftools 1.9
bwa 0.7.17
samtools 1.9
snpeff 5.1
tabix 1.9
trimmomatic 0.39
varscan 2.4.4
vcftools 0.1.16
```